dreamtools 1.2.5

Scoring functions for the DREAM / SAGE challenges

Note:

DREAMTools is compatible for Python 2.7, 3.3, 3.4, 3.5

Note about coverage:

We do not run the entire test suite on Travis, which reports a 40% test coverage. Note however, that the actual test coverage is about 80%.

Contributions:

Please join https://github.com/dreamtools/dreamtools and share your notebooks https://github.com/dreamtools/dreamtools/notebooks

Online documentation:

On pypi website

Issues and bug reports:

On github

How to cite:

Cokelaer T, Bansal M, Bare C et al. DREAMTools: a Python package for scoring collaborative challenges [version 1; referees: awaiting peer review] F1000Research 2015, 4:1030 (doi: 10.12688/f1000research.7118.1) F1000 link

Contents

• Overview

  • Motivation

  • Usage

• Installation

  • Familiar with Python ecosystem ?

  • If you are new to Python

  • Installation from source

• The dreamtools executable

• Available challenges

• Gold standards

• Issues

• Contributions

• For developers

• Credits

• More documentation ?

Overview

Motivation

DREAMTools aims at sharing code used in the scoring of DREAM challenges that pose fundamental questions about system biology and translational medicine.

The main goals of DREAMTools are to provide:

1. scoring functions equivalent to those used during past DREAM challenges for end-users via a standalone application (called dreamtools).

2. a common place for developers involved in the DREAM challenges to share code

DREAMTools does not provide code related to aggregation, leaderboards, or more complex analysis even though such code may be provided (e.g., in D8C1 challenge).

Note that many scoring functions requires data hosted on Synapse . We therefore strongly encourage you to register to Synapse. Depending on the challenge, you may be requested to accept terms of agreements to use the data.

Usage

DREAMTools can be used by developers as a Python package:

>>> from dreamtools import D6C3
>>> s = D6C3()
>>> s.score(s.download_template())
{'results': chi2            53.980741
R-square        34.733565
Spearman(Sp)     0.646917
Pearson(Cp)      0.647516
dtype: float64}

A standalone application can be used from a terminal. The executable is called dreamtools. Here is an example:

dreamtools --challenge D6C3 --submission path_to_a_file

See below for more details about the usage of the standalone application.

Installation

Although there is a dedicated documentation related to the installation of DREAMTools (in doc/source/installation.rst), we provide here below a brief summary.

Familiar with Python ecosystem ?

If you are familiar with Python and the pip application and your system is already configured (compilers, development libraries available)), these two commands should install DREAMTools and its dependencies (in unix or windows terminal):

pip install cython
pip install dreamtools

If you are new to Python

If you are not familiar with Python, or have issues with the previous method (e.g., compilation failure), or do not have root access, we would recommend to use the Anaconda solution.

Anaconda is a free Python distribution. It includes most popular Python packages for science and data analysis. Anaconda will install most of the software required by DREAMTools. Besides, since it does not require root access, it should not interfere with your system.

You will need to choose between 2 versions of Python (2.X or 3.5). Since DREAMTools is compatible with Python 2.7 and 3.5, the version should not matter. Note, however, that for Windows’ users, we would recommend to use Python 2.7 (see installation for explanations).

Here below are 4 steps checked on Unix and Windows platforms.

For Mac and Linux users:

1. Download Anaconda

2. Open an Anaconda shell (or a unix shell)

3. Download conda_install.sh

4. Execute the script (e.g. for Python2):

   sh conda_install.sh python=2

Similarly for For Windows:

1. Download Anaconda2 (Python2) for windows

2. Open an Anaconda prompt (from the Start->All program->Anaconda2->Anaconda Prompt

3. Download conda_install.bat

4. Execute the script:

   conda_install.bat

If there is an issue, please visit the installation page (doc/source/installation.rst) where details about the installation scripts can be found.

Installation from source

The command:

pip install dreamtools

install the latest release of DREAMTools. If you prefer to use the source code, you can also get the github repository and install DREAMTools as follows (dependencies such as numpy or scipy will need to be compiled if not found):

git clone [e-mail]:dreamtools/dreamtools.git
cd dreamtools
python setup.py install

The dreamtools executable

DREAMTools provides functions to obtain the template and gold standard(s) used in a given challenge. Some challenge have restrictions of data access and require the user to accept conditions of use. Such data are stored on http://www.synapse.org. You will need to create a login/password on www.synapse.org website. The first time you run a challenge within DREAMTools, files will be downloaded from Synapse. You may be asked to accept some conditions of use (e.g. D8C1 challenge) directly on the website.

For users, DREAMTools package provides an executable called dreamtools, which should be installed automatically.

To obtain some help, type:

dreamtools --help

You should see a list of challenges: D2C1,D2C3, D2C3,… Those are aliases to DREAM challenges. Information about a challenge can be (in general) obtained from the Synapse page of the challenge using the –onweb option:

dreamtools --challenge D6C3 --onweb

Brief information can also be printed in the terminal as follows:

dreamtools --challenge D6C3 --info

Next, you may want to score one of your submission. We provide access to templates for each challenge. For instance:

dreamtools --challenge D6C3 --download-template

This command prints the location of the template on your system. Copy that file in local/temporary place. Now that you have a copy of the template, you can fill its contents with your own data and score it (let us assume it is called D6C3_template.txt):

dreamtools --challenge D6C3 --submission D6C3_template.txt

This command should print some information and the score of the submission for instance for the example above, we get the following results:

{'results': chi2            53.980741
 R-square        34.733565
 Spearman(Sp)     0.646917
 Pearson(Cp)      0.647516
 dtype: float64}

All outputs will contain a json-like output. The synapse page of the challenge should give information about the scoring methodology.

Note that some challenges (like the D8C1 challenge) have sub-challenges. For instance in D8C1, there are 4 sub-challenges names (e.g., SC1A). So, you would need to be more specific and to provide the name of a sub-challenge. For instance:

dreamtools --challenge D8C1 --download-template --sub-challenge SC1A

Note

In D8C1, you will also need to accept the conditions of use of the data on a Synapse page, which should pop up.

The sub-challenge names can be obtained using –info option (see here above). Similarly to the simpler case shown above, you can now score that submission as follows:

dreamtools --challenge D8C1 --sub-challenge SC1A \
    --submission D8C1_example.zip

Again, you should get an output with the results:

Solution for alphabeta-Network.zip in challenge d8c1 (sub-challenge sc1a) is :
meanAUROC: 0.803628919403

Available challenges

DREAMTools includes about 80% of DREAM challenges from DREAM2 to DREAM9.5 Please visit F1000 link (Table 1).

Gold standards

All gold standards are retrieved automatically. You can obtain the location of a gold standard file as follows:

dreamtools --challenge D6C3 --download-goldstandard

Issues

Please fill bug report in https://github.com/dreamtools/dreamtools/issues

Contributions

Please join https://github.com/dreamtools/dreamtools

For developers

Please see doc/source/developers.rst

Credits

Please see doc/source/credits.rst

More documentation ?

Please see the doc directory, which is processed and posted on pypi website with each release.